Title: A Lecture on High-Throughput Sequencing Using a Specific Scenario and Clicker
Questions
Jenifer Cruickshank
Affiliations:
State University of New York at Oswego, Oswego, New York
Type of Manuscript: CourseSource Lesson Manuscript
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Abstract Page
The abstract should be a single paragraph of 250 words or less. Start with an opening sentence
that sets the teaching challenge that you address in this manuscript, provide background
information specific to this Lesson, briefly description the Lesson, and end with a concluding
sentence.
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Article Context Page: To make the submission
process easier, you may want to fill out the
following form, (you will be asked to select
answers during the submission process). Choose all
applicable options that effectively describe the
conditions IN WHICH THE LESSON WAS
TAUGHT. Modifications to expand the usability of
the Lesson will be addressed later in the text.
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in those cases, please select ‘N/A’ when
submitting on the website.
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Course
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Lesson Length
o Portion of one class period
o One class period
o Multiple class periods
o One term (semester or quarter)
o One year
o Other
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Key Scientific Process Skills
o Reading research papers
o Reviewing prior research
o Asking a question
o Formulating hypotheses
o Designing/conducting experiments
o Predicting outcomes
o Gathering data/making
observations
o Analyzing data
o Interpreting results/data
o Displaying/modeling results/data
o Communicating results
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Pedagogical Approaches
o Think-Pair-Share
o Brainstorming
o Case Study
o Clicker Question
o Collaborative Work
o One Minute Paper
o Reflective Writing
o Concept Maps
o Strip Sequence
o Computer Model
o Physical Model
o Interactive Lecture
o Pre/Post Questions
o Other

Bloom’s Cognitive Level (based on
learning objectives & assessments)
o Foundational: factual knowledge &
comprehension
o Application & Analysis
o Synthesis/Evaluation/Creation
Biochemistry
Cell Biology
Developmental Biology
Genetics
Microbiology
Molecular Biology
Introductory Biology
Course Level
o Introductory
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Class Type
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Audience
o Life Sciences Major
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o Non-Traditional Student
o 2-year College
o 4-year College
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Class Size
o 1 – 50
o 51 – 100
o 101+
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Principles of how people learn
o Motivates student to learn material
o Focuses student on the material to
be learned
o Develops supportive community of
learners
o Leverages differences among
learners
o Reveals prior knowledge
o Requires student to do the bulk of
the work

Vision and Change Core Concepts
o Evolution
o Structure and Function
o Information flow, exchange and
storage
o Pathways and transformations of
energy and matter
o Systems
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Vision and Change Core Competencies
o Ability to apply the process of
science
o Ability to use quantitative
reasoning
o Ability to use modeling and
simulation
o Ability to tap into the
interdisciplinary nature of science
o Ability to communicate and
collaborate with other disciplines
o Ability to understand the
relationship between science and
society
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Key Words: List 3 – 10 key words that are
relevant for the Lesson (e.g. mitosis;
meiosis; reproduction; egg; etc.)
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Scientific Teaching Context Page
Learning Goal(s):
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Students will understand the basic processes of next-generation sequencing (NGS) and sequence analysis.
Students will appreciate what kinds of research questions can be answered with information garnered from
NGS data.
Provide clearly stated learning goals, which are broad statements of what the students will know once
they have completed the Lesson. Learning goals are typically rather abstract and use words like
“know,” “understand”, “appreciate,” or “demonstrate”.
For example:
 Students will understand the steps in mitosis.
 Students will appreciate the importance of mitosis in the process of reproduction.
Learning Objective(s):
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Choose an appropriate sequencing technology for a particular research question.
Define the types of differences one would look for when comparing two genome sequences.
Define what students who have successfully accomplished the learning goal can actually do. Learning
objectives describe student behaviors that are observable, measurable, and testable. Learning
objectives should test students’ mastery of the material and use words like “define”, “predict”,
“design” and “evaluate.”
For example:
 Compare and contrast mitosis and meiosis.
 Predict consequences of abnormal meiosis.
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Main Text
Begin the Lesson text on a new page. Include the following sections:
1. Introduction:
This lesson is intended to introduce students to next-generation sequencing (NGS) technologies, the
types of data NGS generates, and why one would be interested in large-scale sequence information.
The set-up of the lesson is a clicker-based lecture that will present a scenario at the start of class that
progresses (virtually) through (re)sequencing, assembling, and analyzing a eukaryotic genome, then
comparing the newly-generated genome to the pre-existing genome sequence of a closely-related
species.
This lesson is intended for one lecture period (80 minutes) in a Genetics course. Enrolled students
are primarily second and third year undergraduate biology and zoology majors with a smaller
proportion of biochemistry majors. This class period would be late in the semester when students
should have a solid understanding of DNA structure, what a gene is, eukaryotic gene structure, and
basic principles of evolution. Students will prepare specifically for this lecture by reading several
relevant sections on genomics in the course textbook and by watching several online videos on
different sequencing techniques (Sanger, Illumina, NanoPore?)
The introduction should provide the origin and rationale for the design of the Lesson and provide enough
background information to allow the reader to evaluate the Lesson without referring to extensive
outside material. For complex topics, a Science Behind the Lesson article may be simultaneously
submitted with the Lesson, so that potential instructors will have sufficient information to
implement the Lesson.
The introduction should also explain:
 Intended Audience: Describe the intended student population for the Lesson, including level
and major affiliation. For example: first-year students, biology majors, non-majors, advanced
biology students, etc.
 Learning time: Indicate the approximate class or lab time required for the Lesson, keeping in
mind potential alternate Lesson timelines that may also be described in the modifications
section.
 Pre-requisite student knowledge: Describe the knowledge and skills that students should have
before using this Lesson. Prerequisite knowledge may include both science process skills and
background content knowledge.
2. Scientific Teaching Themes:
Active Learning: Students will actively engage with the material with clicker questions, which will
be of the “What should be our next step?” variety. A clicker question will be posed, students will
answer without discussion. Assuming a small minority answer correctly, a mini-lecture on the
subtopic will be presented followed by student discussion with a neighbor then a reposing of the
question. There will be a homework question asking for another specific application of highthroughput sequencing.
Assessment: The clicker questions will provide an assessment of students’ own learning in addition
to assessment information for the instructor. A homework assignment after the class will ask
student to expand beyond the specific example from the lecture. Subsequent exams will include
questions over the material covered in this lecture.
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Inclusive Teaching: Answers to clicker questions are anonymous and allow full participation by
students regardless of their level of extroversion. The follow-up homework question allows
students to identify an application of high-throughput sequencing that is of interest to them.
Explain how the Lesson relates to the Scientific Teaching Themes of:
 Active Learning: How will students actively engage in learning the concepts? List and/or
explain the active learning strategies that are used in the Lesson. For example, activities could
include think-pair-share, clicker questions, group discussion, debate, etc. Include both inclass and out-of-class activities.
 Assessment: How will teachers measure learning? How will students self-evaluate their
learning? List and/or explain the kinds of assessment tools used to measure how well students
achieved the learning objectives. For example, assessments might be clicker questions, forced
choice questions, exams, posters, etc.
 Inclusive Teaching: How is the Lesson designed to include all participants and acknowledge
the value of diversity in science? List and/or explain how the Lesson is inclusive and how it
leverages diversity in the classroom and beyond. For example, the lesson may use multiple
senses and provide examples of scientists from different backgrounds.
3. Lesson Plan:
Pre-class preparation:
Because of the lengthy run times for most eukaryotic genome analysis software programs, all
necessary analyses will have already been done and be accessible during class. In this case, it is
whole genome sequence from a yak. Access to the internet during class is also necessary. Visual
lecture information and clicker questions will be presented on PowerPoint slides.
In-class:
The set-up: A rich hobby farmer wants to know if the yak (Bos grunniens) bull she just purchased
is pure yak or whether he has any cattle (Bos taurus) in his pedigree. She is willing to pay for any
needed “DNA tests” to answer this question.
Clicker question 1: What would be good to know at this point? (Granted, this one is a bit of a
gimme.)
A. Is yak genome information available?
B. Is cattle genome information available?
C. Can we see a picture of the bull?
D. Both A and B would be good to know.
Presumably, D is chosen by a large majority which prompts an internet source by the instructor for
“yak genome” and “cattle genome”. The yak genome search should turn up the Yak Genome
Database, and there are multiple options for the cattle genome, I would go with Ensembl.
Information from the front page of the Yak Genome Database notes the size of the genome (2657
Mb) and that coverage is 65X, prompting
Clicker question 2: What does 65X coverage mean?
A. Every base is present 65 times in the yak sequence data.
B. On average, a given base is present 65 times in the yak sequence
data.
C. 65 yak genomes were sequenced.
D. 65% of the yak genome is included in this yak sequence data.
Presumably, B is not chosen by a large majority which prompts a minilecture on the process of
high-throughput sequencing with examples of Illumina and NanoPores(?).
Repose clicker question 2.
Continue the narrative, we get a blood sample from the yak and extract the DNA (it’s really good
quality). Now what?
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Clicker question 3: What do we do with the DNA?
A. Sequence the mRNAs from this blood sample.
B. Sequence the DNA on an Illumina platform.
C. PCR a few genes and run the PCR products on a gel.
D. Sequence the mtDNA.
Depending on how students answer, briefly review high-throughput sequencing and discuss
incorrect answers.
Continue the narrative: we prepare and send the DNA away for sequencing. Show what the data
files look like when they come back.
Clicker question 4: What should we do with this data first?
A. Assemble the sequences into contigs.
B. Blast the sequences against the database.
C. Assemble the sequences into one long DNA sequence.
D. Assess the quality of the sequences.
Presuming a majority do not correctly choose D, give a mini-lecture on how sequencing errors can
arise and how they can be identified (phred scores and kmer graphs).
Repose clicker question 4.
(Yet to be completed.) Continue along through genome assembly, gene annotation, and
comparative genomics. The final clicker question may be what parts of the genome should we
compare to find out if the yak bull has cattle DNA. Certain genes? coding sequence? introns?
SNPs? Followed by discussion on that topic.
Provide a detailed description of the Lesson that is sufficiently complete and detailed to enable another
teacher to replicate it. You may need/want to include subsections such as: pre-class preparation
and in-class script. A Table containing a recommended timeline for the class should be
included. As needed, expand upon aspects of scientific teaching that are particularly highlighted
in the Lesson. As appropriate, provide examples of formative and/or summative assessments and
related rubrics. List materials that are necessary or useful for teaching the Lesson, whether they
are provided as supplementary materials or as links to other websites.
4. Teaching Discussion:
Data unavailable at this time.
Share your observations about the Lesson’s effectiveness in achieving the stated learning goals and
objectives, student reactions to the Lesson, and your suggestions for possible improvements or
adaptations to different courses or student populations.
 Subheadings: can be included within the sections above to increase readability and clarity.
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Acknowledgments
Begin the Acknowledgements on a new page. The acknowledgements can be multiple
paragraphs.
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References
Begin the References on a new page.
* Cite references in the text using superscript Arabic numbers. Use commas to separate multiple
citation numbers. Superscript numbers are placed outside periods and commas and inside colons and
semicolons.
1. Begin the reference list on a new page. The reference list is comprehensive and spans the text, figure
captions and materials.
2. Number references in the order in which they appear in the text. Follow ASM style and abbreviate
names of journals according to the journals list in NCBI. List all authors and/or editors up to 6; if
more than 6, list the first 3 followed by “et al.” Note: Journal references should include the issue
number in parentheses after the volume number.
Examples of reference style:
1. Knight JK, Wood WB. 2005. Teaching more by lecturing less. Cell Biol Educ. 4(4):298-310.
2. Samford University. How to get the most out of studying: A video series.
www.samford.edu/how-to-study/. Accessed August 20, 2013.
3. Handelsman J, Miller S, Pfund C. 2006. Scientific Teaching. New York, NY:W.H. Freeman.
3. Please add notes to the end of the reference list; do not mix in references with explanatory notes.
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Tables:
Table 1. Table legends should contain a short description of the table.
Figures:
Figure 1. The figure legend should begin with a sentence that describes the overall “take home
message” of the figure. Figure parts are indicated with capital letters (A).
Supplementary Materials: (Follow descriptions for Tables and Figures, listed above.)
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